...as Admin like to be able to "file" certain PMs for ease of future reference - things like reported PMs, long running discussions with certain members (usually troublemakers), Moderator discussions, PMs with useful information in them. On phpbb.com I like to file PMs relating to my extensions separately.

just trying to understand everything you are changing with the UI as I have to take it into consideration for the development of the new UI for the new theme and would like to get a better idea to of what you are think to be able to provide better feedback on how to implement it to meet both versions.

I am not sure what that is meant to represent but judging by the ticks I an guessing that the panel on the left is a list of messages and that the bottom panel on the right is the message content - so what is the panel top right?

Personally I would prefer the left panel to be a list of folders, the top right a list of messages in the slected folder and the bottom right the message content.

Ideally it would be good if this was user configurable but that is perhaps a step too far

DavidRemember: You only know what you know -
and you do not know what you do not know!

I'd rather work with "collapsible" directories on the left side, smaller checkmarks, an indicator if the destination user is online (means probable quick answer) (cannot bypass invisible!). Each directory has multiple messages, a scroll to scroll through the messages and a "search filter" kind of thing to filter titles, sender or receiver.
That, if I understood right how you are planning that.

The left panel is similar to how different conversations are currently being displayed, one panel for each conversation. Forgot the scroll bar.
(We can probably just display all in a single panel)
I need to think about the folders although reconfigurability is probably out of the scope.

I'd rather work with "collapsible" directories on the left side, smaller checkmarks, an indicator if the destination user is online (means probable quick answer) (cannot bypass invisible!). Each directory has multiple messages, a scroll to scroll through the messages and a "search filter" kind of thing to filter titles, sender or receiver.

The tick marks are just place-holders for some sort of indication as to whether the messages have been read. (Since we will be merging inbox/outbox)
I'm no designer(clearly), hanakin probably has a good idea for this.
Darkened boxes are meant to represent unread messages.